title: RD_siRNA_LSD1-3, biological replicate 3

city: Frankfurt am Main

first: Simone

last: Fulda

state: Hessen

address: Komturstraße 3A

department: Institute for experimental cancer research in pediatrics

institute: Goethe University Frankfurt

description: CountsTable_RNASeq_RD_Ctrl_vs_LSD1-3.xlsx

data_processing:
We aligned these reads to the hg19 build of the human genome using Tophat
The aligned reads were counted with the homer software (analyzeRNA) and edgeR
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

source_name: Rhabdomyosarcoma

growth_protocol: RD cells were cultured in DMEM supplemented with 10% fetal calf serum, 1 % Penicillin/Streptomycin and 1% Pyruvat, splitted twice a week upon reaching confluency and seeded in 15 cm dishes (Corning) at a density of 15000 cells / cm² for the RNA Sequencing experiments.

extract_protocol:
RNA was extracted using PeqGOLD Total RNA Extraction Kit (PeqLab, Erlangen, Germany) according to the manufacturer's instructions.
RNASeq library was prepared according to the standard protocol with Illumina TrueSeq Library Preparation Kit.

treatment_protocol: RD cells were reversly transfected with Silencer Select siRNA against LSD1 (Invitrogen, construct s618 corresponds to siRNA LSD1-2, construct s619 corresponds to siRNA LSD1-3) or siControl (Invitrogen, cat no. 4390842) using Lipofectamine RNAiMAX reagent and OptiMEM (both Life technologies) with culture media exchange after 8 hours of transfection. Transfected cells were grown for 96 hours until harvesting.

value: RD cells

tag: passages

tag: knockdown construct

value: Silencer select siRNA (Invitrogen, target:KDM1A, construct s619)

tag: experiment/run

value: Experiment/Run 2 (siRNA LSD1-3)


title: RD_siRNA_LSD1-3, biological replicate 2

status: Public on Nov 07 2019

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: RD_siRNA_Ctrl_for1-3, biological replicate 3

value: Silencer select siRNA (Invitrogen, cat no. 4390842)

value: Experiment/Run 2 (siRNA Ctrl to siRNA LSD1-3)


title: FAST4-CTRL ASO-4

city: Minneapolis

first: Douglas

middle: Gene

last: Mashek

state: Minnesota

address: Suite 6-155, 321 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

country: USA

institute: University of Minnesota

description:
Sample_ID-PE-4_S56
Sample.ID.PE.4
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the mouse genome (mm10) as a reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: subread_dmashek: Tab-delimited text file includes feature counts.
Supplementary_files_format_and_content: genes.fpkm_table_dmashek: Tab-delimited text file includes FPKM values.

organism: Mus musculus

source_name: Liver

growth_protocol: Purified normal diet.

extract_protocol:
RNA was extracted using the RNeasy Kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CTRL/PLIN5 ASO for gene silence.

tag: tissue

value: Liver

tag: aso

value: Control

tag: feeding

value: Fasted


title: KO_GV_4

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

country: China

institute: tongji university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

source_name: Zcchc8 KO_GV oocytes

extract_protocol:
2-5embryos were collected as one replicate. Zona pellucida of embryos were removed with 0.5% protease E (Sigma). Embryos were washed for 5-6 times in 0.5% BSA(Sigma) in PBS solution before put into cell lysis buffer. After incubation at 70°C for 90 seconds, reverse transcription for the first strand cDNA was performed subsequently with a 24 oligo (dT) primer. After second strand cDNA synthesis, cDNA library was amplified for 16-18 cycles based on the embryo number. Amplified cDNA was diluted for 10 times for qPCR reaction.
For library construction, amplified cDNA was sheered to 200-300 bp using Covaris S220 system. The sequence libraries were generated using KAPA HyperPlus Library Preparation kit (Roche, KK8510), following the manufacturer’s instructions. 8-12 cycles amplification was used depending on cDNA concentration.

tag: strain

value: GV oocytes

tag: genotype/variation

value: Zcchc8 KO


title: RD_siRNA_LSD1-2, biological replicate 3

description: CountsTable_RNASeq_RD_Ctrl_vs_LSD1-2.xlsx

value: Silencer select siRNA (Invitrogen, target:KDM1A, construct s618)

value: Experiment/Run 1 (siRNA LSD1-2)


title: RD_siRNA_Ctrl_for1-3, biological replicate 2


title: RD_siRNA_Ctrl, biological replicate 3

value: Experiment/Run 1 (siRNA Ctrl to siRNA LSD1-2)


title: RD_siRNA_Ctrl_for1-3, biological replicate 1


title: RD_siRNA_LSD1-2, biological replicate 1


title: RD_siRNA_LSD1-3, biological replicate 1


title: Input_H3K4me2_siRNA_LSD1_RD_Rep2

library_source: genomic

data_processing:
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using Bowtie
peak finding algorithm MACS
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are wiggle and bed files. The wig files include the read data mapped to the hg19 genome. The bed files contain the peaks that were obtained when normalizing the reads of the ChIP-Seq to the Input. Data is provided separately for each biological replicate and as pooled data from both replicates.

molecule: genomic DNA

growth_protocol: RD cells were cultured in DMEM supplemented with 10% fetal calf serum, 1 % Penicillin/Streptomycin and 1% Pyruvat, splitted twice a week upon reaching confluency and seeded in 15 cm dishes (Corning) at a density of 15000 cells / cm² for the ChIP Sequencing experiments.

extract_protocol:
Genomic DNA was extracted by manual lysis with a douncer for nuclear extraction followed by sonification (Covaris, M220). DNA-Histone-complexed were precipated with antibody against H3K4me2.
ChIPSeq library was prepared according to the standard protocol with Illumina TrueSeq Library Preparation Kit.

treatment_protocol: RD cells were reversly transfected with Silencer Select siRNA against LSD1 (Invitrogen, construct s618) or siControl (Invitrogen, cat no. 4390842) using Lipofectamine RNAiMAX reagent and OptiMEM (both Life technologies) with culture media exchange after 8 hours of transfection. Transfected cells were grown for 96 hours until harvesting.

tag: cell line

tag: knockdown

tag: chip antibody


title: RD_siRNA_LSD1-2, biological replicate 2


title: RD_siRNA_Ctrl, biological replicate 1


title: ChIP_H3K4me2_siRNA_LSD1_RD_Rep2

value: anti-rabbit H3K4me2 (Diagenode, Liège, Belgium)


title: RD_siRNA_Ctrl, biological replicate 2


title: ChIP_H3K4me2_siRNA_Ctrl_RD_Rep2


title: Input_H3K4me2_siRNA_Ctrl_RD_Rep2


title: ChIP_H3K4me2_siRNA_LSD1_RD_Rep1


title: ChIP_H3K4me2_siRNA_Ctrl_RD_Rep1


title: Line 2, Ground rep2 [GB5]

city: Stanford

first: Joseph

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
Raw reads were aligned by HISAT2 (https://ccb.jhu.edu/software/hisat2/index.shtml)(Kim et al., 2015) to human genome (hg38).
Aligned reads were quantitated by FeatureCounts (http://bioinf.wehi.edu.au/featureCounts/) with the annotation of ENSEMBL 85.
Normalization and differentially expressed genes test were implemented by DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) (Liao et al., 2014; Love et al., 2014).
Supplementary_files_format_and_content: table of normalized log2 transformed expression.

source_name: hiPSC-CM_ground control, no microgravity exposure

growth_protocol: Three hiPSC lines were generated using a previously published Sendai virus reprogramming protocol on peripheral blood mononuclear cells from three healthy individuals (Churko et al., 2013). These hiPSC lines were differentiated into hiPSC-CMs using a 2D monolayer differentiation protocol and were maintained in a 5% CO2/air environment as previously described (Lian et al., 2012; Sun et al., 2012)

extract_protocol:
RNALater (Thermo Fisher) was used to preserve flight samples designated for downstream RNA-sequencing analysis. Samples preserved in RNALater were stored at 4°C until return to our laboratory, when RNA was isolated from preserved wells in the BioCells using RNeasy kit (Qiagen) following the manufacturer’s protocol. DNase treatment was performed using RNase-free DNase kit (Qiagen). All RNA samples had RNA integrity number ≥ 8.9 and concentration ≥ 48 ng/µL (Agilent 2100 Bioanalyzer).
Library prep and sequencing were performed by BGI with 30-40 million paired-end 100bp reads per sample on the Illumina HiSeq platform.

tag: cell line sournce

value: hiPSC line2

value: hiPSC-derived cardiomyocytes

tag: treatment


title: Line 3, Ground rep2 [GB6]

value: hiPSC line3

value: ground control, no microgravity exposure


title: Input_H3K4me2_siRNA_LSD1_RD_Rep1

value: RD cells


title: Input_H3K4me2_siRNA_Ctrl_RD_Rep1


title: Line 1, Ground rep2 [GB4]

value: hiPSC line1


title: Line 3, Ground rep1 [GB3]


title: Line 2, Ground rep1 [GB2]


title: Line 1, Ground rep1 [GB1]


title: Line 3, Post-flight rep2 [FC6]

source_name: hiPSC-CM_5.5 weeks microgravity exposure, followed by 10 days normal gravity


title: Line 2, Post-flight rep2 [FC5]

value: 5.5 weeks microgravity exposure, followed by 10 days normal gravity


title: Line 1, Post-flight rep2 [FC4]


title: Line 2, Flight rep2 [FB5]

source_name: hiPSC-CM_4.5 weeks microgravity exposure

value: 4.5 weeks microgravity exposure


title: Line 2, Post-flight rep1 [FC2]


title: Line 3, Flight rep2 [FB6]


title: Line 3, Post-flight rep1 [FC3]


title: Line 1, Flight rep2 [FB4]


title: Line 1, Post-flight rep1 [FC1]


title: Line 3, Flight rep1 [FB3]


title: M857-P010_G

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline54. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2. Duplicate reads were removed using SAMBLASTER before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5. To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0  to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K4me3, H3K27ac and H3K4me1 and MACS version 2.1 p-value threshold of 1e-5 were used to idenftify H3K27me3, H3K9me3 and H3K79me2 enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Melanoma Tumor Sample

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC).  ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

treatment_protocol:
Melanoma tumors were obtained from the Melcore tumor bank at MD Anderson Cancer Center.
Tissue was disassociated (50 mg of tissue; ~8 mg per histone modification antibody) manually in 2 mL of Hanks' Balanced Salt Solution (HBSS) using a sterile razor blade. Mince the tissue into 3 to 4 mm pieces for approximately 5 min in a sterile tissue culture dish. Transfer the tissue and HBSS solution into a dissociator tube and add another 8 mL of HBSS. Further disassociate the tissue using a dissociator until homogenized. For melanoma tumors, place the tubes in a dissociator and run the following cycles each one time in this order: h_tumor_01.01, h_tumor_02.01, h_tumor_03.01 and m_heart_02.01.

value: Tissue


title: M857-P010_D

tag: chip-antibody

value: H3K79me2 Abcam ab3594


title: M857-P010_F

value: H3K27me3 Abcam ab6002


title: M857-P010_E

value: H3K4me3 Abcam ab8580


title: M852-P008_D


title: M852-P008_E


title: M852-P008_B

value: H3K9me3 Abcam ab8898


title: Line 2, Flight rep1 [FB2]


title: M822-P010_B


title: M822-P010_D


title: M822-P010_F


title: M857-P010_B


title: M807-P010_D


title: M807-P010_G


title: M807-P010_E


title: M807-P010_F


title: M807-P010_B


title: M762-P008_D


title: M762-P008_E


title: M822-P010_G


title: M852-P008_F


title: M749-P010_G


title: M762-P008_F


title: M762-P008_B


title: M852-P008_G


title: M822-P010_E


title: M749-P010_B


title: M749-P010_D


title: M749-P010_E


title: M721-P010_G


title: M721-P010_B


title: M721-P010_E


title: M721-P010_F


title: M721-P010_D


title: M762-P008_G


title: M642-P008_F


title: M642-P008_E


title: M527-P010_E


title: M527-P010_G


title: M749-P010_F


title: M527-P010_D


title: M642-P008_D


title: M642-P008_B


title: M409-P011_F


title: M527-P010_B


title: M409-P011_G


title: M409-P011_D


title: wl_sml2 R2

city: Canberra

first: Li

last: Wang

state: ACT

address: North-Science Road, Acton ACT 2601

country: Australia

institute: CSIRO

data_processing:
The quality control reports of each sequencing sample were provided by the sequencing provider.
Alignment of sequenced reads was performed using STAR version 2.5.3a against the TAIR10 reference genome and and the araport11 annotation.
The mapped counts were normalized according to the library size across all the samples.
Genome_build: TAIR10 reference genome and and the araport11 annotation
Supplementary_files_format_and_content: Text File - Gene ID and counts of associated aligned reads (pre-normalised counts) for all samples

organism: Arabidopsis thaliana

source_name: wl_sml2_rosette leaves of 25 day-old plants

growth_protocol: Arabidopsis hybrid seeds [Wassilewskija (Ws)/Landsberg erecta (Ler), Col/Ler and C24/Ler] were produced by hand-pollination between parental accessions. Ws/Ler and Col/Ler Hybrid Mimic lines and F7 small plant lines were produced from the recurrent selection protocol. Sterilized seeds were sown onto plates with Murashige and Skoog (MS) medium (Murashige and Skoog Basal Salts with minimal organics, Sigma-Aldrich, M6899) supplemented with 3% (wt/vol) sucrose and 0.8% wt/vol agar, pH5.7. Seeds were kept at 4 °C in the dark, then transferred into a growth room with conditions of 16h light (22°C)/8h dark (18°C) and light density at 120 -150 μmol photons m-2·s-1. Plate-grown seedlings were transferred into soil at 15 days after sowing.

extract_protocol:
The rosette leaves of 25 day-old plants were sampled. RNA was extracted by a Maxwell RSC robot using RNA extraction kit (Promega, Maxwell RSC plant RNA kit, AS1500).
illumina

tag: genetic background

tag: age

value: 25 day-old plants

value: rosette leaves


title: wl_sml2 R1


title: wl_sml2 R3


title: M409-P011_B


title: M409-P011_E


title: M642-P008_G


title: wl_sml1 R2

source_name: wl_sml1_rosette leaves of 25 day-old plants


title: wl_sml1 R3


title: WL_HM7 R2

source_name: WL_HM7_rosette leaves of 25 day-old plants


title: M527-P010_F


title: WL_HM7 R3


title: wl_sml1 R1


title: M399-P010_F


title: M399-P010_D


title: M399-P010_E


title: M399-P010_G


title: IL12RKO_HPOS_D2_001

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

source_name: splenic NK cells

extract_protocol:
Cells were sorted directly into Trizol and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.

value: splenic NK cells

tag: genotype

tag: replicate

value: HPOS

tag: condition


title: WL_HM6 R3

source_name: WL_HM6_rosette leaves of 25 day-old plants


title: M357-P010_G

tag: cell type


title: WL_HM6 R1

tag: tissue


title: WL_HM6 R2


title: M399-P010_B


title: M357-P010_F


title: WL_HM5 R3

source_name: WL_HM5_rosette leaves of 25 day-old plants


title: WL_HM5 R2


title: M357-P010_E


title: WL_HM5 R1


title: WL_HM3 R3

source_name: WL_HM3_rosette leaves of 25 day-old plants


title: WL_HM4 R3

source_name: WL_HM4_rosette leaves of 25 day-old plants


title: WL_HM4 R1


title: M306-P008_G


title: M357-P010_D


title: WL_HM4 R2


title: WL_HM3 R2


title: M306-P008_F


title: WL_HM2 R3

source_name: WL_HM2_rosette leaves of 25 day-old plants


title: WL_HM7 R1


title: WL_HM2 R2


title: M306-P008_E


title: WL_HM2 R1


title: M306-P008_D


title: WL_HM1 R3

source_name: WL_HM1_rosette leaves of 25 day-old plants


title: WL_HM1 R2


title: cl_sml2 R3

source_name: cl_sml2_rosette leaves of 25 day-old plants


title: M306-P008_B


title: cl_sml2 R2


title: M357-P010_B


title: M305-P009_G


title: M305-P009_F


title: cl_sml2 R1


title: cl_sml1 R3

source_name: cl_sml1_rosette leaves of 25 day-old plants


title: cl_sml1 R2


title: M305-P009_D


title: cl_sml1 R1


title: CL_HM6 R3

source_name: CL_HM6_rosette leaves of 25 day-old plants


title: M305-P009_B


title: CL_HM6 R2


title: M275-P008_G


title: WL_HM3 R1


title: M275-P008_F


title: CL_HM6 R1


title: CL_HM5 R3

source_name: CL_HM5_rosette leaves of 25 day-old plants


title: CL_HM5 R2


title: WL_HM1 R1


title: M275-P008_B


title: M275-P008_D


title: CL_HM5 R1


title: M305-P009_E


title: M263-P011_E


title: M263-P011_D


title: CL_HM3 R2

source_name: CL_HM3_rosette leaves of 25 day-old plants


title: CL_HM4 R2

source_name: CL_HM4_rosette leaves of 25 day-old plants


title: CL_HM3 R3


title: CL_HM4 R1


title: CL_HM3 R1


title: M263-P011_F

source_name: Melanoma Tumor Sample


title: CL_HM2 R3

source_name: CL_HM2_rosette leaves of 25 day-old plants


title: M275-P008_E


title: M263-P011_B


title: M233-P010_G


title: WT_GV_4

source_name: wild type_GV oocytes

value: GV oocytes

value: wild type


title: M233-P010_F


title: CL_HM1 R3

source_name: CL_HM1_rosette leaves of 25 day-old plants


title: CL_HM2 R1


title: CL_HM1 R2


title: CL_HM4 R3


title: M263-P011_G


title: LerxWs F1 R2

source_name: LerxWs F1_rosette leaves of 25 day-old plants

value: LerxWs F1


title: LerxWs F1 R3


title: M233-P010_E


title: LerxWs F1 R1


title: M233-P010_B


title: M233-P010_D


title: WsxLer F1 R3

source_name: WsxLer F1_rosette leaves of 25 day-old plants

value: WsxLer F1


title: M137-P008_F


title: WsxLer F1 R2


title: CL_HM2 R2


title: WsxLer F1 R1


title: LerxCol F1 R3

source_name: LerxCol F1_rosette leaves of 25 day-old plants

value: LerxCol F1


title: M137-P008_D


title: LerxCol F1 R1


title: M137-P008_B


title: M035-P010_G


title: ColxLer F1 R2

source_name: ColxLer F1_rosette leaves of 25 day-old plants

value: ColxLer F1


title: M137-P008_E


title: LerxCol F1 R2


title: CL_HM1 R1


title: ColxLer F1 R1


title: ColxLer F1 R3


title: Ws R3

source_name: Ws_rosette leaves of 25 day-old plants

value: Ws


title: M035-P010_D


title: Ws R2


title: M137-P008_G


title: M035-P010_B


title: Ler R2

source_name: Ler_rosette leaves of 25 day-old plants

value: Ler


title: Ler R3


title: Col  R3

source_name: Col _rosette leaves of 25 day-old plants

value: Col


title: M028-P008_F

value: Tissue


title: M028-P008_G


title: Ler R1


title: Col  R1


title: M028-P008_E


title: Ws R1


title: Mutant seedlings, 50 μM JA treatment for 3 h_3

city: beijing

first: Changjiang

last: Li

address: Yuanmingyuan West Road 2,Haidian

department: College of Biological Sciences

institute: China Agricultural University

description: m-3 h-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidospsis whole genome using TopHat2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM were calculated using a protocol as blow: exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.Cufflinks software was using to caculate the FPKM value.
Cufflinks was used for assembling transcripts and analyzing differential expression of indicated samples .
Genome_build: TAIR10 (ftp://ftp.ensemblgenomes.org/pub/release-35/plants/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz)
Supplementary_files_format_and_content:  tab-delimited text files include FPKM values

source_name: Whole seedling

growth_protocol: Seeds were sterilized with 5% (v/v) sodium hypochlorite for 15 min and then placed in 4 degree for 3 d before sowing. Young seedlings before transferring to soil were grown on 1/2 MS (Murashige and Skoog medium with 1% sucrose) culture plate in incubator with 16 h light /8 h dark photoperiod at 22°C.

extract_protocol:
Samples were collected at indicated time in liquid nitrogen and total RNA was extracted by RNA extraction kit (TIANGEN, China)
5 ug RNA of each sample was used for library construction and Illumina Hiseq 2500 platform was used for RNA-deep sequencing

treatment_protocol: Wild type and ecap-2 seedling grown for 6-day-old on 1/2 MS plate was transferred to plate containing 50 μM JA for 0, 1 and 3 hours.

tag: developmental stage

value: six day-old seedling

value: ecap-2 mutant

value: JA

tag: time (treatment period)

value: 3 h


title: Mutant seedlings, 50 μM JA treatment for 3 h_2

description: m-3 h-2


title: Mutant seedlings, 50 μM JA treatment for 3 h_1

description: m-3 h-1


title: Mutant seedlings, 50 μM JA treatment for 1 h_3

description: m-1 h-3

value: 1 h


title: M035-P010_F

value: H3K27me3 Abcam ab6002


title: Mutant seedlings, 50 μM JA treatment for 0 h_3

description: m-0 h-3

value: untreated

value: 0 h


title: Mutant seedlings, 50 μM JA treatment for 1 h_2

description: m-1 h-2


title: M028-P008_B

value: H3K9me3 Abcam ab8898


title: M-WM793B_E

source_name: CCLE Cell Line

value: Cell Line

value: H3K4me3 Abcam ab8580


title: Mutant seedlings, 50 μM JA treatment for 0 h_2

description: m-0 h-2


title: M-WM793B_F


title: M-WM793B_D

value: H3K79me2 Abcam ab3594


title: Mutant seedlings, 50 μM JA treatment for 1 h_1

description: m-1 h-1


title: M-WM793B_B


title: Mutant seedlings, 50 μM JA treatment for 0 h_1

description: m-0 h-1


title: Col  R2

value: 25 day-old plants

value: rosette leaves


title: M-WM266_F


title: M-WM266_G


title: M-WM266_E


title: Wild type seedlings,50 μM JA treatment for 3 h_2

description: Col-3 h-2

value: Wild type


title: M-WM266_D


title: Wild type seedlings,50 μM JA treatment for 3 h_3

description: Col-3 h-3


title: M028-P008_D


title: M-WM266_B


title: Wild type seedlings,50 μM JA treatment for 3 h_1

description: Col-3 h-1


title: Wild type seedlings,50 μM JA treatment for 1 h_3

description: Col-1 h-3


title: M-WM793B_G


title: M-WM165_G


title: Wild type seedlings,50 μM JA treatment for 1 h_1

description: Col-1 h-1


title: Wild type seedlings, Control_3

description: Col-0 h-3


title: M-WM165_F


title: M-WM165_D


title: Wild type seedlings,50 μM JA treatment for 1 h_2

description: Col-1 h-2


title: Wild type seedlings, Control_2

description: Col-0 h-2


title: M-WM165_B


title: M-WM115_D


title: M-WM115_B


title: M-WM115_E


title: M-WM115_F


title: Wild type seedlings, Control_1

description: Col-0 h-1


title: M-HS934_G


title: R304_Naive

city: Herston

first: Susanna

last: Ng

state: QLD

address: 300 Herston Road

department: Immunology

institute: QIMR Berghofer Medical Research Institute

data_processing:
Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a)
Sequence reads were aligned to the GRCh37 assembly with the gene, transcript, and exon features of Ensembl (release 89) gene model
Quality control metrics were computed using RNA-SeQC (version 1.1.8)
Expression was estimated using RSEM (version 1.2.30)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-seperated values file includes unfiltered, normalised counts per million (cpm)

source_name: PBMCs

extract_protocol:
Cells were homogenised in QIAshredder (QIAGEN) columns, followed by RNA extraction using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions. Total RNA was treated with the RNase-free DNase Set (QIAGEN).
mRNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs). Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Trial participants were treated with the investigational Medicinal Product (IMP) (+)-SJ000557733 (SJ733) at day 7 p.i.

tag: participant id

value: Blood

tag: timepoint

value: Day 14 p.i.

value: Tneg cells


title: R302_TR1

value: Tr1 cells


title: R402_TR1


title: R304_TR1


title: R302_Naive


title: R402_EFF

value: Th1 cells


title: M-WM165_E


title: M-HS934_E


title: M-HS934_D


title: R302_EFF


title: M-HS934_B


title: R301_TR1


title: M-WM115_G


title: M-G361_G


title: R301_Naive


title: M-G361_F


title: R301_EFF


title: R002_TR1


title: M-G361_E


title: M-G361_D


title: M-HS934_F


title: R002_Naive


title: R002_EFF


title: R001_TR1


title: M-A2058_G


title: M-G361_B


title: R402_Naive


title: M-A2058_F


title: M-A2058_D


title: R001_EFF


title: Glioblastoma cells, Rictor-KD 2

city: Shinjuku

first: Kenta

last: Masui

state: Tokyo

address: 8-1 Kawada-cho

department: Department of Pathology

country: Japan

institute: Tokyo Women's Medical University

data_processing:
Illumina HiSeq Control Software 2.2.38, RTA 1.18.61, bcl2fastq 1.8.4, used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using trimmomatic v0.32, then mapped to hg38 whole genome using bwa v0.7.10 with default parameters.
Read Counts were calculated using samtools v.0.1.19.
Genome_build: hg38
Supplementary_files_format_and_content: ReadCounts.txt includes read count values for each Sample.

source_name: Glioblastoma cells

growth_protocol: U87-EGFRvIII GBM cell lines were cultured in DMEM supplemented with 10% FBS (Omega Scientific, Tarzana, CA) in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
Total RNA was isolated by RNeasy Plus Mini Kit (QIAGEN, Venlo, The Netherlands).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: U87-EGFRvIII cells were treated with siRNA  (Santa Cruz, Dallas, TX) against Scramble sequence or Rictor for 48 hours.

tag: cell line

value: U87-EGFRvIII glioblastoma cell line

tag: RNAi treatment

value: Rictor

value: Rictor knockdown


title: Glioblastoma cells, Scramble 2

value: Scramble

value: control


title: M-A2058_E


title: M-96_G


title: R001_Naive


title: Glioblastoma cells, Rictor-KD 1


title: M-96_F

value: H3K27me3 Abcam ab6002


title: M-96_E

value: Cell Line


title: M-A2058_B

value: H3K9me3 Abcam ab8898


title: M-96_D

value: H3K79me2 Abcam ab3594


title: Glioblastoma cells, Scramble 1


title: WT.1

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq 2500 instrument.
The raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using the Illumina bcl2fastq program version 2.17. One mis-match was allowed for index sequence identification.
Adapter trimming was performed using BBDuk (https://jgi.doe.gov/data-andtools/bbtools/), and read pairs were merged with BBmerge (https://jgi.doe.gov/data-and-tools/bbtools/) in order to increase base call quality and generate long, whole fragment reads.
Reads were aligned to the human genome (hg38) and the respective HIV-1 genome sequence (provided in percent_usage_splice_junction_data.xlsx) simultaneously using Hisat2.
HIV-mapping, splice junction spanning reads were isolated using regtools (https://github.com/griffithlab/regtools) to allow per junction read counting.
Genome_build: hg38 with the respective HIV-1 genome sequence added as an additional “chromosome”
Supplementary_files_format_and_content: Spreadsheet containing HIV-1 splice junction coordinates (donor and acceptor site coordinates) w.r.t. the HIV-1 genome sequence, splice junction names, and a percent usage value for each junction in each sample, calculated by dividing the junction spanning read count by the total number of junction spanning reads in the respective sample.

molecule: polyA RNA

source_name: transfected HeLa cells

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin. All cell lines were grown at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
48h after transfection, cells were washed with 1x PBS and lysed. The RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s instructions.
The multiplexed RNA sequencing library was prepared using the TruSeq Stranded mRNA library Prep kit following the manufacturer’s protocol (Illumina, Cat# RS-122-2101).

treatment_protocol: HeLa cells were seeded in a 6 well plate and transfected at a confluency of 70%. HeLa cells were transfected using TransIT-LT1 (Mirus) according to the manufacturer’s instructions at the ratio of 3 μL TransIT-LT1 to 1μg DNA.

value: HeLa

tag: hiv-1 genotype

value: wildtype


title: WT.2


title: CM22-378.2


title: CM22-378.1


title: M-940_G


title: M-96_B


title: R304_EFF


title: CM22-261.2


title: CM22-261.1


title: CM22-165.1


title: M-940_D


title: M-84_G


title: M-940_B


title: M-940_E

value: H3K4me3 Abcam ab8580


title: KRAS-3

city: La Jolla

first: Jonathan

middle: Ross

last: Hart

state: CA

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

data_processing:
Basecalling with Cassava 1.8
Alignment to genome using RNA STAR 2.6.0b.  Exact parameters are STAR --genomeDir ${genome} --readFilesIn $fq1 \      --readFilesCommand zcat --runThreadN 12 --genomeLoad NoSharedMemory \      --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \      --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 \      --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \      --outSAMunmapped Within --outFilterType BySJout \      --outSAMattributes NH HI AS NM MD \      --outSAMtype BAM Unsorted \      --quantMode TranscriptomeSAM GeneCounts \      --outFileNamePrefix $prefix --outTmpDir $scratch/star
Sorted alignments using Sambamba v0.5.4 Exact command line: sambamba sort -t 12 -m 26G --tmpdir=$scratch -l 9 -o $outBam $inBam
Counted alignments with HTSEQ-count v0.9.1 Exact command line: htseq-count -f bam -r pos --max-reads-in-buffer 100000000 -s yes $array > $out
Genome_build: hg38.d1.vd1
Supplementary_files_format_and_content: Raw counts of alignments to Gencode version 27

source_name: breast epithelial cells

growth_protocol: 500k Cells were seeded in 10cm petri dishes in DMEM/F12 growth medium. After 24 hours, medium was changed to MCDB-170 serum free media. Cells were allowed to grow an additional 24 hours. Medium was changed once more and cells harvested at 6 hours post medium exchange.

extract_protocol:
Cells were then harvested by suspending them with trypsin and neutralized with soybean trypsin inhibitor (ThermoFisher), and total RNA isolated using the Maxwell RSC simplyRNA cells kit (Promega), as per the manufacturer’s instructions.
Total RNA was ribosome depleted and libraries were constructed by Genewiz following Illumina protocols.

treatment_protocol: No drug treatment

tag: kras status

tag: pik3ca  status

value: WT

value: breast epithelial cells


title: KRAS-1


title: M-84_D

tag: chip-antibody


title: DKI5-3


title: KRAS-2


title: M-84_B


title: M-84_E


title: DKI5-2


title: M-61_G


title: M-84_F


title: DKI5-1


title: NETSeq timepoint Q2

city: Oxford

first: Jack

middle: Edward

last: Feltham

state: Oxfordshire

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during early HOC (-20 min from minimum O2%)
column header in processed data file:
Q2
NETSeq-counts.csv

data_processing:
Data was aligned to a combined cerevisiae/pombe genome using bowtie
Unique reads were extracted using samtools
Counts tables were generated using custom scripts.
Genome_build: SacCer3 + ASM294v2
Supplementary_files_format_and_content: counts tables (.csv)
Library strategy: NET-seq

organism: Saccharomyces cerevisiae

source_name: NETSeq timepoint Q2

growth_protocol: Cells were inocluated into a Bioflo320 fermenter containing 1.1 l YMC-YE media maintained at pH 3.5. Cells were grown to saturation (OD600~ 16.0), starved for >2 hrs then fed fresh YMC-YE at 1.5/1.2 ml/min to induce metabolic cycling.

extract_protocol:
Harvested cells were spiked with frozen S. pombe powder and lysed using a Retsch Mixer Mill. Samples were DNase-digested and RNA was extraced from RNAPII that had been immunoprecipitated using anti-FLAG antibodies.
Libraries were constructed as in Fischl et al., 2017

treatment_protocol: Dissolved oxygen levels in the chamber were monitored and samples were taken at time intervals relative to the point of lowest dissolved oxygen for a particular cycle.

tag: strain

value: CENPK113-7D rpb3-FLAG

tag: treatment

value: Metabolic cycling at 1.5 ml/min in 1.1l vessel


title: M-940_F


title: M-61_D


title: M-61_E


title: NETSeq timepoint Q1

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (-10 min from minimum O2%)
column header in processed data file:
Q1
NETSeq-counts.csv

source_name: NETSeq timepoint Q1


title: M-61_F


title: CM22-165.2


title: M-57_G


title: NETSeq timepoint Y10

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during mid LOC (+120 min from minimum O2%)
column header in processed data file:
Y10
NETSeq-counts.csv

source_name: NETSeq timepoint Y10


title: NETSeq timepoint Y8

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during mid LOC (+95 min from minimum O2%)
column header in processed data file:
Y8
NETSeq-counts.csv

source_name: NETSeq timepoint Y8


title: M-61_B


title: NETSeq timepoint Y7

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (0 min from minimum O2%)
column header in processed data file:
Y7
NETSeq-counts.csv

source_name: NETSeq timepoint Y7


title: NETSeq timepoint Y6

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during early HOC (-25 min from minimum O2%)
column header in processed data file:
Y6
NETSeq-counts.csv

source_name: NETSeq timepoint Y6


title: M-57_F


title: M-57_D


title: M-57_E


title: NETSeq timepoint Y5

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during early HOC (-30 min from minimum O2%)
column header in processed data file:
Y5
NETSeq-counts.csv

source_name: NETSeq timepoint Y5


title: NETSeq timepoint Y4

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during mid LOC (+50 min from minimum O2%)
column header in processed data file:
Y4
NETSeq-counts.csv

source_name: NETSeq timepoint Y4


title: M-57_B


title: NETSeq timepoint Y2

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during early LOC (+35 min from minimum O2%)
column header in processed data file:
Y2
NETSeq-counts.csv

source_name: NETSeq timepoint Y2


title: NETSeq timepoint Y3

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during late HOC (+13 min from minimum O2%)
column header in processed data file:
Y3
NETSeq-counts.csv

source_name: NETSeq timepoint Y3


title: Batch RiboSeq

description:
rpf
A RiboSeq library generated from BY4741 growing exponentially in YPD to mid-log phase (OD600 = 0.6)
CENPK113-7D_rpb3-FLAG_RiboSeq.bed

data_processing:
Data was trimmed using cutadapt to remove linker sequences then aligned to a combined cerevisiae/pombe genome using tophat
Unique reads were extracted using samtools and data was converted to .bed format
Metagenes were generated using custom R scripts.
Genome_build: SacCer3 + ASM294v2
Supplementary_files_format_and_content: .bed files
Library strategy: Ribo-Seq

source_name: Batch RiboSeq

extract_protocol:
Harvested cells were spiked with frozen S. pombe powder and lysed using a Retsch Mixer Mill. Lysate was digested with RNaseI and monosomes were isolated using SEC.
Libraries were constructed according to Ingolia et al., 2012

value: Log-phase growth in YPD


title: M-52_G


title: M-52_E


title: M-52_F


title: NETSeq timepoint Y1

description:
Nascent RNA
A NETSeq library generated from cycling CENPK113-7D rpb3-FLAG during late HOC (+20 min from minimum O2%)
column header in processed data file:
Y1
NETSeq-counts.csv

source_name: NETSeq timepoint Y1


title: M-52_B

source_name: CCLE Cell Line


title: M-52_D


title: YMC RiboSeq

description:
rpf
A RiboSeq library generated from cycling CENPK113-7D during early LOC phase (+30min from minimum O2%)
BY4741_log_RiboSeq.bed

source_name: YMC RiboSeq


title: M-48_G


title: M-48_F


title: Q24_231

city: Guangzhou

first: Jian

last: Shi

state: Guangdong

address: 1023 South Shatai Road

institute: Southern Medical University

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: The text file includes rawcounts for each samples

source_name: Breast

growth_protocol: MDA-MB-231 breast cancer cells were cultured in Dulbecco's Modified Eagle Medium containing 10% FBS and Penicillin/streptomycin.

extract_protocol:
Total RNA was harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: MDA-MB-231 breast cancer cells were treated with DMSO or JQ1 (1 μM) for 24 hours.

value: Breast cancer cell line

value: JQ1 treatment for 24 hours


title: C_231

value: DMSO treatment


title: SF_WT_7

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: SF WT 7

data_processing:
RNA-seq aligned to hg19 genome and UCSC reference transcript using STAR (version 2.4.0).
Expression analysis performed by Featurecounts (version 1.5.0).
Bigwig generated after normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

source_name: MDS bone marrow_SF WT

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
TruSeq RNA Sample Preparation Kit (Illumina) was used for library preparation.

value: Myelodysplastic syndromes (MDS) bone marrow

tag: splice factor mutation

value: None (wild type)

tag: who subtype


title: M-48_B


title: SF_WT_8

description: SF WT 8

value: RA


title: M-22_G

value: Cell Line


title: SF_WT_6

description: SF WT 6


title: M-22_F

value: H3K27me3 Abcam ab6002


title: SF_WT_2

description: SF WT 2


title: SF_WT_3

description: SF WT 3

value: RCMD


title: M-22_D

value: H3K79me2 Abcam ab3594


title: M-22_E


title: SF_WT_1

description: SF WT 1


title: ZRSR2_4

description: ZRSR2 mutant 4

source_name: MDS bone marrow_ZRSR2 mutant

value: ZRSR2 mutation E104fs


title: M-22_B

value: H3K9me3 Abcam ab8898


title: ZRSR2_2

description: ZRSR2 mutant 2

value: ZRSR2 mutation H330Y


title: M-12_G


title: M-48_E

value: H3K4me3 Abcam ab8580


title: M-12_E


title: M-48_D


title: U2AF1_8

description: U2AF1 mutant 8

source_name: MDS bone marrow_U2AF1 mutant

value: U2AF1 mutation Q157P

value: RCMD-RS


title: SF_WT_4

description: SF WT 4


title: SF_WT_5

description: SF WT 5


title: M-12_B


title: U2AF1_7

description: U2AF1 mutant 7

value: U2AF1 mutation S34F


title: U2AF1_6

description: U2AF1 mutant 6


title: 2812-STC1_G

source_name: Melanoma Short Term Cultures


title: WT_SC_rep2

first: Xin

state: shanghai

address: 320 Yue Yang Road, Shanghai 200031

institute: Shanghai Institute of Biochemistry and Cell Biology

description:
Larp7_SC_A3SS.MATS.txt
Larp7_SC_A5SS.MATS.txt
Larp7_SC_MXE.MATS.txt
Larp7_SC_RI.MATS.txt
Larp7_SC_SE.MATS.txt

data_processing:
Raw reads were mapped to mm10 genone using STAR(parameters offered by rMATS)
The bam files were then used to analyzed differential alternative splicing events using rMATS
Differential alternative splicing events (|psi|≥0.05, fdr<0.05) were selected for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include alternative splicing events for each Sample.

source_name: Wildtype spermatocytes

extract_protocol:
Mouse spermatocytes and round spermatids were isolated from adult mouse testes by FACS. In brief, total spermatogenic cells were extracted from the seminiferous tubules of adult male mice, stained by Hoechst 33342 (Acros Organics), and then separated through FACS sorting. The isolated spermatogenic cells were further confirmed by their distinct nuclear morphology (DAPI staining of nuclei). Total RNAs were extracted from mouse spermatocytes and round spermatids using RNAiso Plus (Takara)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Wildtype

value: mouse spermatocytes


title: U2AF1_5

description: U2AF1 mutant 5


title: U2AF1_4

description: U2AF1 mutant 4

value: U2AF1 mutation Q157R


title: WT_SC_rep1


title: 2812-STC1_E

tag: cell type


title: 2812-STC1_D


title: WT_RS_rep1

description:
Larp7_RS_A3SS.MATS.txt
Larp7_RS_A5SS.MATS.txt
Larp7_RS_MXE.MATS.txt
Larp7_RS_RI.MATS.txt
Larp7_RS_SE.MATS.txt

source_name: Wildtype round spermatids

value: mouse round spermatids


title: WT_RS_rep2


title: U2AF1_3

description: U2AF1 mutant 3

tag: tissue

value: Myelodysplastic syndromes (MDS) bone marrow

value: U2AF1 mutation R156H


title: 2812-STC1_B

value: Cell Line


title: U2AF1_2

description: U2AF1 mutant 2

value: U2AF1 mutation S34Y

value: RA


title: M-12_F

value: H3K27me3 Abcam ab6002


title: ZRSR2_3

description: ZRSR2 mutant 3

value: ZRSR2 mutation T411fs

value: RCMD


title: M-12_D

value: H3K79me2 Abcam ab3594


title: ZRSR2_1

description: ZRSR2 mutant 1

value: ZRSR2 mutation Y373X


title: U2AF1_1

description: U2AF1 mutant 1


title: 2792-STC1_F


title: 2812-STC1_F


title: M035-P010_E

source_name: Melanoma Tumor Sample

value: Tissue

value: H3K4me3 Abcam ab8580


title: Larp7_SC_rep1

source_name: Larp7 knock-out spermatocytes

value: Larp7 knock-out


title: SRSF2_5

description: SRSF2 mutant 5

source_name: MDS bone marrow_SRSF2 mutant

value: SRSF2 mutation P95_R102del


title: Larp7_RS_rep1

source_name: Larp7 knock-out round spermatids


title: SRSF2_6

description: SRSF2 mutant 6

value: SRSF2 mutation R150fs


title: 2792-STC1_E


title: SRSF2_4

description: SRSF2 mutant 4


title: IgG_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using cutadapt(-a AGATCGGAAGAGCACACGTCT -A GATCGTCGGACTGTAGAACTCTGAAC)
Processed reads were mapped to mm10 genome by bowtie2 with default paremeters
Gene expression were counts by rsem
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts, FPKM and TPM values for each Sample.

source_name: 8 weeks mouse testes

extract_protocol:
RNA Immunoprecipitation (RIP)  assays were performed with standard RIP protocols. In brief, mouse testes  were homogenized in lysis buffer [50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% Triton X-100, 5 mM EDTA, 1 x Complete Mini, RNase inhibitor(Thermo) and proteinase Inhibitor cocktail (Roche)]. Primary antibody-coupled Protein A/G beads were added to the precleared tissue  and incubated for 4 hr at 4 °C. After washed with washing buffer [50 mM Tris-HCl (pH 7.4), 500 mM NaCl, 0.1% Triton X-100, 5 mM EDTA, RNase inhibitor(Thermo) and proteinase inhibitor cocktail]
RNA libraries were prepared for sequencing using NEBNext® Multiplex Small RNA Library Prep Set for Illumina protocols. Size selection for 15-300nt RNAs.

tag: rip antibody

value: IgG(Millipore, 12-370)


title: IgG_rep1


title: 2765-STC1_G


title: 2792-STC1_D


title: Islets, HFD mice 3 (lncRNA-seq)

city: nnajing

first: fangfang

last: zhang

address: 24 Tongjiaxiang, Nanjing, Jiangsu province, People's republic of China

institute: China Pharmaceutical University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, The reads mapped to the mouse genome (GRCM38/mm10) were analyzed using GEM software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: sample.txt:  tab-delimited text file includes FPKM values for each Sample

source_name: islet

extract_protocol:
islet were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: islet

value: post 8-week high-fed diet


title: SRSF2_3

description: SRSF2 mutant 3

value: Myelodysplastic syndromes (MDS) bone marrow

value: SRSF2 mutation P95R

value: RCMD-RS


title: Larp7_rep2

value: LARP7(abcam, ab134757)


title: SRSF2_2

description: SRSF2 mutant 2

value: SRSF2 mutation P95H


title: 2792-STC1_G

value: Cell Line


title: SRSF2_1

description: SRSF2 mutant 1

value: RCMD


title: 2765-STC1_E


title: 2792-STC1_B

value: H3K9me3 Abcam ab8898


title: Islets, HFD mice 2 (lncRNA-seq)


title: Islets, HFD mice 1 (lncRNA-seq)


title: 2765-STC1_F

value: H3K27me3 Abcam ab6002


title: SF3B1_5

description: SF3B1 mutant 5

source_name: MDS bone marrow_SF3B1 mutant

value: SF3B1 mutation K666N


title: Larp7_RS_rep2

value: mouse round spermatids


title: Islets, NCD mice 3 (lncRNA-seq)

value: post 8-week normal chow diet


title: 2765-STC1_D

value: H3K79me2 Abcam ab3594


title: SF3B1_4

description: SF3B1 mutant 4

value: SF3B1 mutation K700E

value: RARS


title: Islets, NCD mice 2 (lncRNA-seq)

value: islet


title: SF3B1_3

description: SF3B1 mutant 3


title: 2761-STC1_G


title: 2765-STC1_B


title: Islets, NCD mice 1 (lncRNA-seq)


title: SF3B1_2

description: SF3B1 mutant 2

value: SF3B1 mutation K666T


title: SF3B1_1

description: SF3B1 mutant 1

value: Myelodysplastic syndromes (MDS) bone marrow

value: SF3B1 mutation H662Q


title: Larp7_rep1


title: 2761-STC1_F


title: ATAC-KO-2

description: processed data file: GSE127790_KO-ATAC.bw

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using bowtie2 (v 2.2.9) command with default parameters.
MACS14 (v 1.4.2) with default parameters was used for peak finding with parameter --nomodel --shiftsize 25.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig file were generated using MACS2(v 2.0.10) pileup function.

source_name: Embryonic stem cells

extract_protocol:
Samples were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.15%NP-40) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500g for 5 min to remove the supernatant.
Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme Biotech). After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. PCR was performed to amplify the library for 15 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; following by 72 °C 5 min. After the PCR reaction, libraries from 200bp to 700bp were purified from gel extraction before sequencing.

value: derived ESC

tag: genotype/variation

value: Zcchc8 KO


title: ATAC-KO-1


title: ATAC-WT-2

description: processed data file: GSE127790_WT-ATAC.bw

value: wild type


title: 2761-STC1_D

value: Cell Line


title: KD_Replicate2-1

city: Hefei

first: Kun

last: Qu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

description: total RNA

data_processing:
The CRISPR library was generated with sgRNAs designed against each of the 2,263 epidermally-expressed lncRNAs using the SSC algorithm optimized for CRISPR interference. The genomic interval from -50 to +450 relative to the transcriptional start site (TSS) was used for each target lncRNA.
For RNA-seq, raw reads were uniquely mapped to hg19 using STAR with default parameter. Bedtools were used to transform the mapped bam file into bedGraph. RPKM and raw reads count were calculated by self-designed scripts with ensemble annotation(Homo_sapiens.GRCh37.gtf). The differential expression analysis was performed using Deseq.
For CRISPRi screening sequencing data, raw reads were mapped to the library using  MAGeCK (0.5.5). To identify the top negatively and positively selected lncRNAs, MAGeCK “test” command was performed.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM expression matrix of basal and suprabasal with gene class annotation is in tab seperated format, which includes the following columns: GeneSymbol, GeneClass, basal_rep1, basal_rep2, suprabasal_rep1, suprabasal_rep2. CRISPRi library contains all designed sgRNAs with linker sequences. Raw read counts file is in tab seperated format, which includes the following columns: Transcript_id, GeneSymbol, C1_1, C1_2, C2_1, C2_2, K1_1, K1_2, K2_1, K2_2.

source_name: neonatal foreskin

growth_protocol: Primary epidermal progenitor were isolated from discarded neonatal foreskin from circumsticions. After isolation, cells were grown in a 50:50 mixture of K-SFM and Medium 154 with supplements recommended by the manufacturer (Life Technology). All cells were incubated at 37°C in 5% CO2 and grown at a maximal confluence of 70-80%.

extract_protocol:
Total RNA was isolated using the Direct-zol RNA kit (Zymo research), treated with DNase I and mRNA was enriched by oligo(dT) magnetic beads (Invitrogen). Upon fragmentation, double-stranded cDNA was synthesized using random hexamer-primer and reverse transcriptase (Invitrogen) and purified with magnetic beads. End reparation and 3’-end single nucleotide adenine addition was then performed.
Sequencing adaptors are ligated to the fragment and enriched by PCR amplification and size-selected (~200 bp). During the QC step, Agilent 2100 Bioanalyzer and ABI StepOnePLus Real-Time PCR are used to quantify the sample library. The resulting product was subjected to RNA-Seq on the Illumina HiSeqTM 4000, using 50 bp single reads.

treatment_protocol: Cells were infected with lentivirus generated from the pLKO.1 vector (RNAi consortium) containing shRNA sequences targeting LINC01481 (KD) or scrambled (control), in medium containing 3 µg/ml polybrene and incubated overnight. Infected cells were selected using 1 µg / ml puromycin.

tag: cell-type

value: Human epidermal progenitors


title: KD_Replicate2-2

institute: University of Science and Technology of China

description: total RNA


title: ATAC-WT-1


title: 2698-STC1_G

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline54. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2. Duplicate reads were removed using SAMBLASTER before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5. To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0  to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K4me3, H3K27ac and H3K4me1 and MACS version 2.1 p-value threshold of 1e-5 were used to idenftify H3K27me3, H3K9me3 and H3K79me2 enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC).  ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.


title: R4: the liver of rat with CCl4 combined with BK channel activator rottlerin treatment 4

type: RNA

city: Shanghai

first: Linli

last: Yang

address: Shanghai ,Xianxia Road 720#

institute: Shanghai Jiaotong University

description: Gene expression data from liver subjected to BK channel activator lower than fibrotic liver

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

label: biotin

organism: Rattus norvegicus

source_name: fibrotic liver with BK activaor treatment

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: 9 liver tissues came from rat

extract_protocol: Total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Directly after anaesthesia, the partial liver tissues were subjected to liquid nitrogen treatment and then stored at -80°C.

value: liver


title: R6: the liver of rat with CCl4 combined with BK channel activator rottlerin treatment 6


title: R5: the liver of rat with CCl4 combined with BK channel activator rottlerin treatment 5


title: KD_Replicate1-2

description: total RNA


title: RNA_KO_Zcchc8_2

first: You

address: 1239 siping road

institute: tongji university

data_processing:
Illumina Casava1.8 software used for basecalling.
For RNA seq, sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

growth_protocol: ESC derived from blastocysts (BDF1 strain) were cultured in ESC medium: DMEM (Gibco),15% fetal bovine serum (Hyclone), nucleosides (100×),1 mM l-glutamine,1% nonessential amino acid stock, 0.1 mM mercaptoethanol, 1,000 U/ml LIF (Merk Millipore), 3 m CHIR99021 (S2924; Selleck) and 1 M PD0325901 (S1036; Selleck).

extract_protocol:
Total RNA was obtained from at least 5×10^5 ESCs via RNeasy Mini Kit extraction(Qiagen).
For total RNA (rRNA erased), 1μg total RNA were used for RNA-seq with the KAPA RiboErase Kit (Roche) following the manufacturer’s instructions.

value: Zcchc8 KO and Zcchc9 overexpression


title: KD_Replicate1-1

description: total RNA


title: C1: the liver of rat with CCl4 treatment 1

description: Gene expression data from fibrotic liver higher than vehicle liver

source_name: fibrotic liver


title: C3: the liver of rat with CCl4 treatment 3


title: C2: the liver of rat with CCl4 treatment 2


title: 2698-STC1_F

value: H3K27me3 Abcam ab6002


title: Control_Replicate2-2

description: total RNA


title: VC4: the liver of rat with vehicel treatment 4

description: Gene expression data from vehicle lower than fibrotic liver

source_name: vehicle liver


title: 2761-STC1_E

value: H3K4me3 Abcam ab8580


title: VC5: the liver of rat with vehicel treatment 5


title: Control_Replicate2-1

description: total RNA


title: 2698-STC1_E


title: RNA_KO_2


title: Control_Replicate1-2

description: total RNA


title: 2761-STC1_B

value: H3K9me3 Abcam ab8898


title: RNA_KO_Zcchc8_1

value: Zcchc8 KO and Zcchc8 overexpression


title: RNA_KO_1


title: RNA_control_2


title: 2698-STC1_B


title: RNA_control_1


title: Day28_Replicate2

description: guide RNA

extract_protocol:
Genomic DNA was isolated from cell pellets using a Genomic DNA Isolation Kit (Qiagen) sgRNAs were quantitated by amplification from genomic DNA using PrimeStar (Clontech) using primers flanking the sgRNA sequence for 20 cycles. The resulting product was column-purifed using a PCR purification kit (Macherey-Nagel). The entire product was amplified in a 7 cycle PCR to introduce Illumina sequencing primers and unique barcodes for eacht experiment. Libraries were quantified using the NEBNext Library Quantitation Kit (New England Biolabs) and mixed equimolar for sequencing.
All designed library sgRNA sequences were prepended and appended with linker sequences (5’ linker: CTTGTGGAAAGGACGAAACACC; 3’ linker: GTTTAAGAGCTATGCTGGAAACAGC) to facilitate polymerase chain reaction amplification and to serve as invariant sequence overhangs for InFusion cloning. The oligonucleotides were synthesized (CustomArray) and delivered as a single oligonucleotide pool. The pool was amplified for 15 cycles (Forward primer: ATCTTGTGGAAAGGACGAAACA, Reverse primer: CTGTTTCCAGCATAGCTCTTAAAC) with CloneAmp HiFi (Clontech). The entire PCR reaction was resolved on a 2% agarose gel, and the product was retreived by gel slice isolation. A lentiviral vector pSICO-(F+E) was derived from the vector pSLQ1651 (Addgene plasmid # 51024) by insertion of a 1.9 kb BsmBI stuffer fragment between the U6 promoter and downstream tracrRNA. InFusion cloning was performed to assemble the sgRNA library into BsmBI-digested pSICO (F+E). Lentivirus was generated by transfection of lentiviral helper plasmids and the CRISPRi plasmid library into 293T cells, and lentiviral supernatant collected 48 hours afterwards. Supernatant was concentrated using Lenti-X Concentrator (Clontech) and frozen at -80°C in replicate aliquots.

treatment_protocol: To introduce expression of dCas9-KRAB, cells were infected with lentivirus generated from pLex-KRAB-dCas9-Blast (Addgene #60954). KRAB-dCas9 expressing cells were selected and infected with the CRISPRi library at a multitude of infection (MOI) of 0.3 and selected. Cells were split upon reaching 70% confluence until reaching 28 days.

tag: expression

value: dCas9-KRAB expressing


title: 2559-STC1_G


title: 2559-STC1_F


title: VC3: the liver of rat with vehicel treatment 3


title: 2559-STC1_E


title: Day28_Replicate1

description: guide RNA


title: 2559-STC1_D

value: H3K79me2 Abcam ab3594


title: GRN2_hi

first: Julia

last: Marschallinger

address: 1201 Welch Road

department: Neurology

institute: Stanford University

description: BODIPY-high microglia (lipid-droplet rich)

data_processing:
Sequencing of isolated microglia was carried out with Novaseq 6000, paired end, 2x 100 bp depth sequencer.
The quality of fastq files was assessed using FASTQC (v 0.11.4).
Reads were mapped to mouse mm9 reference genome using STAR (v 2.5.3a).
Raw read counts were generated with STAR using the GeneCounts function.
Differential expression analysis was performed using DESeq2 with standard settings.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

extract_protocol:
Primary microglia were isolated by gentle dounce homogenization of the brain, Percoll-based myelin removal, and FACS-purification of ~10,000 live CD11b+CD45lo cells. BODIPYlo (=lipid droplet-low) and BODIPYhi (=lipid droplet-high) microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according to the manufacturer’s protocol.
cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina).

tag: age

value: 10 month old

tag: Sex

value: male


title: 2698-STC1_D

first: Kunal

address: 1801 East Rd

institute: MD Anderson Cancer Center


title: GRN1_hi


title: 2559-STC1_B


title: Control_Replicate1-1

description: total RNA


title: GRN3_lo

description: BODIPY-low microglia (lipid-droplet low)


title: 2549-STC1_G


title: GRN2_lo


title: GRN3_hi


title: GRN1_lo


title: 2549-STC1_F


title: Day0_Replicate2

description: guide RNA


title: C45 TSA 9Gy 48h

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

institute: Kyoto Univ Graduate School of Medicine

description: Gene expression DMSO treated, 0Gy-irradiated tumor organoids

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: C45 CTOS, TSA treated, 48h after 9Gy irradiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: CTOSs were cultured in Matrigel in StemPro hESC SFM (Life Technologies, Carlsbad, CA).

extract_protocol: Total RNA was extracted from CTOSs with TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: Disrupted CTOSs were pre-treated with DMSO or 1 μM TSA for overnight. After removal of reagents, CTOSs were cultured in fresh Stem Pro hESC for 2h, and irradiated at 9 Gy. RNA was extracted at the indicated time points.

value: cultured organoids (CTOS)


title: C45 TSA 9Gy 24h

source_name: C45 CTOS, TSA treated, 24h after 9Gy irradiation


title: Day0_Replicate1

description: guide RNA


title: KO-ICM-3

city: shanghai

last: Wu

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

source_name: inner cell mass in blastocyst

extract_protocol:
2-5embryos were collected as one replicate. Zona pellucida of embryos were removed with 0.5% protease E (Sigma). Embryos were washed for 5-6 times in 0.5% BSA(Sigma) in PBS solution before put into cell lysis buffer. After incubation at 70°C for 90 seconds, reverse transcription for the first strand cDNA was performed subsequently with a 24 oligo (dT) primer. After second strand cDNA synthesis, cDNA library was amplified for 16-18 cycles based on the embryo number. Amplified cDNA was diluted for 10 times for qPCR reaction.
For library construction, amplified cDNA was sheered to 200-300 bp using Covaris S220 system. The sequence libraries were generated using KAPA HyperPlus Library Preparation kit (Roche, KK8510), following the manufacturer’s instructions. 8-12 cycles amplification was used depending on cDNA concentration.

value: inner cell mass in blastocyst

value: Zcchc8-KO oocyte and WT sperm


title: 2549-STC1_D

last: Rai

source_name: Melanoma Short Term Cultures


title: KO-ICM-2


title: 2549-STC1_B


title: KO-ICM-1


title: C45 TSA 9Gy 0h

source_name: C45 CTOS, TSA treated, 0h after 9Gy irradiation


title: 2549-STC1_E


title: 2379-STC1_G


title: Larp7_SC_rep2

last: Wang

source_name: Larp7 knock-out spermatocytes

value: Larp7 knock-out

tag: cell line

value: mouse spermatocytes


title: WT-ICM-3

value: wild type


title: 2379-STC1_F

value: Cell Line


title: C45 DMSO 9Gy 48h

source_name: C45 CTOS, DMSO treated, 48h after 9Gy irradiation


title: C45 TSA 0Gy

source_name: C45 CTOS, TSA treated, 0Gy irradiation


title: WT-ICM-1


title: C45 DMSO 0Gy

source_name: C45 CTOS, DMSO treated, 0Gy irradiation


title: 2379-STC1_D


title: pan_32

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

country: Austria

institute: Medical University of Vienna

data_processing:
Raw fastq files were processed within the NextFlow methylseq pipeline (Dockerfile v.1.3) with --aligner bismark --singleEnd --genome mm10 –rrbs parameters to obtain methylation coverage7°
RnBeads (Muller et al, 2019) were used for quality control and initial analysis of the DNA methylation data according to established practices (Bock, 2012).
We summarized CpGs in 1,000 kb bins and performed differential DNA methylation analysis between amphetamine treatment (n = 5) vs. control (n = 6) or male (n = 5) vs. female (n = 6) datasets using limma (Ritchie et al, 2015) (FDR-adjusted p-value < 0.05, f
The relative over-representation of hypermethylated and hypomethylated tiles was used for GO pathway enrichment analysis (Falcon et al, 2007).
Additionally, we performed base-pair level and region level (for promoters) analysis using methylKit (Akalin et al, 2012)on Bismark methylation call output files. We used both Fisher’s exact test on pooled samples and the chisqr-test with overdispersion f
Genome_build: mm10
Supplementary_files_format_and_content: Methylation signal in bigWig file format

growth_protocol: Each litter was kept equal in size until weaning. Animals were kept in groups of 6 under standard housing conditions with a 12 h/12 h light/dark cycle and food and water available ad libitum. Experiments on live animals conformed to the 2010/63/EU Europea

extract_protocol:
Pancreas samples were homogenized by using a TissueLyser II (Qiagen) with the following settings: 4 x 30sec, 30Hz with RNAse/DNAse-free ceramic beads. Tissues were dissolved in RLT lysis buffer of the DNA/RNA Allprep Kit (Qiagen) following the manufacture
Extracted DNA was subjected to the reduced representation bisulfite sequencing (RRBS) workflow as described previously (Klughammer et al, 2018). One hundred ng of DNA were digested at 37°C for 12 h with 20 units of MspI and TaqI (New England Biolabs) in e

treatment_protocol: On embryonic days (E) 14.5, 15.5 and 16.5, pregnant C57BL/6N mice (Charles River) were injected with amphetamine (n > 10; 10 mg/kg body weight). Offsprings were analyzed after daily in utero exposure to amphetamine. On P0, offspring in each litter was ran

value: Amphetamine

value: Pancreas


title: U1 SHAPE-MaP

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

description: gene-specific amplicons from total RNA

data_processing:
Sequencing and Profile Generation: Purified SLNCR amplicons were pooled and sequenced on an Illumina Miseq instrument, outputting 2 x 300 paired end datasets. For U1 libraries, 2x 150 paired end datasets were generated instead. Reverse transcription of SLNCR yielded three products, corresponding to 3 alternatively spliced forms of SLNCR (SLNCR1: 2257 nt, SLNCR2: 2522 nt, newly observed isoform SLNCR4: 2160 nt). Data from these isoforms were separated before alignment by fragment lengths after merging paired reads. SLNCR1-specific merged reads were then aligned to the SLNCR1/LINC00673 sequence (NCBI Reference NR_036488.1) using the ShapeMapper2 software (Busan and Weeks, 2017; Smola et al., 2015b) with the command shapemapper --target [TARGET].fa --modified --U [MERGED-TREATED-READS].fastq --untreated --U [MERGED-UNTREATED-READS].fastq --denatured --U [MERGED-DENATURED-READS].fastq. When aligning DMS reads, the denatured control was excluded. U1 reads were similarly aligned to the U1 snRNA sequence (NCBI Reference NR_004430.2). SHAPE reactivities are first calculated as a combination of multiple measured mutation rates [(SHAPE treated – untreated)/denatured], and these values are then divided by a normalization factor. Normalization factors are derived via the boxplot method (Hajdin et al., 2013), where reactivities above the larger of the 90th percentile and 1.5 x the interquartile range beyond the 75th percentile are first removed as outliers and the top 10% of remaining reactivities are averaged (the normalization factor). The error of each mutation rate measurement is estimated as (√(mutation rate_nt ) / √(reads_nt )), and then propagated through the combination of rates and normalization to assign a standard error to a SHAPE reactivity.
deltaSHAPE: In-cell SHAPE and DMS protection sites were identified through comparison of in-cell and cell-free reactivities using the ΔSHAPE program with default settings (Smola et al., 2015a; Smola et al., 2016). In-cell data were scaled such that the 95th percentile reactivity matched the average of cell-free 95th percentile reactivities. Significant nt protections were identified in both nuclear and cytoplasmic fractions with the criteria of being centered in window of 5 nt that contains 3 nt with positive smoothed (average of 3 nt window) ΔSHAPE values (cell-free minus in-cell reactivities), positive Z-factors, and standard scores above 1. Additional regions with smoothed ΔSHAPE values above 1 and Z-factors above 0.5 were also considered to account for skewing of Z-score by highly reactive sites. To achieve positive Z-factors, the absolute difference of smoothed in-cell and cell-free reactivities must be greater that 2 times the sum of their smoothed errors (smoothed in quadrature), while a standard score of 1 is achieved when a ΔSHAPE value is more than 1 standard deviation from the mean.
RNA Structure Modeling with SuperFold: RNA partition functions, informed by SHAPE reactivities, were calculated to generate base-pairing probabilities and Shannon entropy (the negative sum of all probabilities multiplied by the natural log of those probabilities) using the SuperFold analysis pipeline (Smola et al., 2015b). For Figure 5, SLNCR1403-780 data were scaled to the U1 normalization factor. The original SLNCR1 data were divided by this U1 normalization factor to obtain U1-scaled reactivity profiles. Low SHAPE, low entropy regions were identified by two methods: [1] as nts where the 50 nt window-median SHAPE and entropy values fall below 0.4 and 0.03, respectively (Figure 5), and [2] nts where the 50 nt window-median SHAPE and entropy values fall below the global medians (Figure S6). Regions separated by 5 or fewer nts were combined and only regions spanning at least 30 nts were retained before expanding to include overlapping base-pairs. RNA secondary structure representations of SLNCR1 were generated from ShapeMapper and SuperFold outputs using VARNA (Darty et al., 2009).
Genome_build: SLNCR1 RNA: NR_036488.1, U1 RNA: NR_004430.2
Supplementary_files_format_and_content: profile.txt files include indicated ShapeMapper outputs, which include read depths, mucleotide mutation rates, raw and normalized SHAPE reactivities, and associated standard errors. Processed fastqs (not raw reads) are the results of parsing raw reads into separate SLNCR isoforms (1, 2, and 4) and merging the associated paired reads: only SLNCR1 reads were used in analysis. Included fasta sequences are files used to align seuqence data while running ShapeMapper sofware.

source_name: WM1976 Melanoma Cells

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS

extract_protocol: [SLNCR MaP]  From each sample of RNA from WM1976 in-cell and cell-free probing experiments, 1-3 µg were subjected to mutational profiling (MaP) reverse transcription (Siegfried et al., 2014; Smola et al., 2015b) using a primer specific to SLNCR. The cDNA generated was buffer exchanged over Illustra microspin G-50 columns (GE Healthcare). Output cDNA (5 µL) was used as a template for 50 µL PCR reactions (Q5 Hot-start polymerase, NEB) with primers made to amplify nt 403-780 of SLNCR1 and add adapter sequences [1x Q5 reaction buffer, 250 nM each primer, 200 µM dNTPs, 3% DMSO, 0.02 Units/µL Q5 Hot-start polymerase]. PCR proceeded in a touchdown format: 98 °C for 2 minutes, 20 cycles of [98 °C for 10 s , 68 °C (decreasing by 1 °C each cycle until reaching 63 °C) for 30 s , 72 °C 30 s], and 72 °C for 2 min. Step 1 PCR products were purified using a 0.8x ratio of Agencourt AMPure XP beads (Beckman Coulter) and eluted in 20 µL of nuclease-free water. Purified PCR products (3 ng) were used as a template in 50 µL of PCR meant to add multiplex indices and remaining sequence necessary for Illumina sequencing [1xQ5 reaction buffer, 500 nM each index primer, 200 µM dNTPs, 3% DMSO, 0.02 Units/µL Q5 Hot-start polymerase]. Step 2 PCR proceeded as follows: 98 °C for 2 minutes, 10 cycles of [98 °C for 10 s , 66 °C for 30 s , 72 °C 20 s], and 72 °C for 2 min. Step 2 PCR products were purified using a 0.8x ratio of Agencourt AMPure XP beads (Beckman Coulter) and eluted in 20 µL of nuclease-free water.  [U1 snRNA MaP]  The procedure for U1 snRNA MaP RT was similar to that of SLNCR MaP with minor modifications: (1) U1-specific primers were used for RT and step 1 PCR, (2) During step 1 PCR, the touchdown protocol began with an annealing temperature of 72 °C and only decreased to 64 °C, and (3) Step 1 PCR included 500 nM of each primer, no DMSO, and only 25 µL of total volume.

treatment_protocol: [Denatured control RNA SHAPE probing]  WM1976 cells were grown in 6-well plates (2 wells per experiment) to ~80% confluency. Media was aspirated, cells were washed once in 1 mL PBS, and total RNA was extracted using 1 mL TRIzol reagent (Thermo Fisher) per well. Resulting total RNA precipitate was resuspended in 30 µL of nuclease-free water. Total RNA (15 µL) was combined with 5 µL of 10x denaturing buffer [500 mM HEPES pH 8, 40 mM EDTA] and 25 µL of formamide, and the mixture was incubated at 95 °C for 1 minute. 5 µL of 10x SHAPE reagent [250 mM 5-nitroisatoic anhydride (5NIA)] was added to the denatured RNA and incubation at 95 °C continued for 1 min. Denatured modified RNA was purified using a 1.8x ratio of Agencourt RNA Clean XP beads (Beckman Coulter) and eluted in 88 µL of nuclease-free water.  [In-cell SHAPE probing]  WM1976 cells were grown in 6-well plates (4 wells per experiment) to ~80% confluency. Cells were washed once in PBS before adding to each well 900 µL of PBS. To two wells, 100 µL of 10x SHAPE reagent [250 mM 5-nitroisatoic anhydride (5NIA)] was added while 100 µL of neat DMSO were added to each of the remaining two wells. Plates were mixed concurrently with reagent addition and then incubated at 37 °C for 10 minutes. Media was aspirated, cells were washed once in 1 mL PBS per well, and total RNA was extracted using 1 mL TRIzol reagent (Thermo Fisher) per well. Resulting pellets were resuspended in 44 µL of water and like wells were combined into 88 µL volumes.   [In-cell DMS probing]  WM1976 cells were grown in 6-well plates (4 wells per experiment) to ~80% confluency. Cells were washed once in PBS before adding to each well 900 µL of DMS Folding Buffer [300 mM Bicine pH 8, 100 mM NaCl, 5 mM MgCl2]. To two wells, 100 µL of 10x DMS reagent [1:5 dimethyl sulfate (DMS): ethanol] was added while 100 µL of neat ethanol were added to each of the remaining two wells. Plates were mixed concurrently with reagent addition and then incubated at 37 °C for 6 minutes. DMS was quenched with 200 µL of beta-mercaptoethanol and cells were placed on ice for 5 minutes. Excess buffer was removed, cells were washed once in 1 mL PBS per well, and total RNA was extracted using 1 mL TRIzol reagent (Thermo Fisher) per well. Resulting pellets were resuspended in 44 µL of water and like wells were combined into 88 µL volumes.  [Cell-Free RNA extraction and protein digestion]  WM1976 cells were grown in two 10 cm dishes to ~80% confluency. Both plates were washed once in 5 mL of PBS before scraping and lysis in 2.5 mL of ice-cold cytoplasmic lysis buffer [40 mM Tris pH 8, 175 mM NaCl, 6 mM MgCl2, 1 mM CaCl2, 256 mM Sucrose, 0.5% Triton-X 100, 0.5 Units/µL RNasin (Promega), 0.45 Units/µl DNase I (Roche)]. Cells were lysed for 5 minutes on ice with intermittent mixing. Cell nuclei were pelleted at 3000 x g for 5 minutes at 4 °C (nuclear fraction), and the resulting supernatant (cytoplasmic fraction) was transferred to a new tube. A volume of 2.5 mL of proteinase K buffer [40 mM Tris pH 8, 200 mM NaCl, 1.5% Sodium Dodecyl Sulfate, and 0.5 mg/mL Proteinase K] was added to the nuclear pellets. The supernatant (cytoplasmic fraction) volume was increased to 5 mL to include a final concentration of 200 mM NaCl, 1.5% Sodium Dodecyl Sulfate, and 0.5 mg/mL Proteinase K (Thermo Fisher). Proteins were digested for 45 minutes at 23 °C with intermittent mixing.  [RNA separation and buffer exchange]  Nucleic acids were extracted twice with 1 volume of Phenol Chloroform Isoamyl Alcohol (25:24:1) that was pre-equilibrated with either 1.1x SHAPE Folding Buffer [110 mM HEPES pH 8, 110 mM NaCl, 5.5 mM MgCl2] or 1.1x DMS Folding Buffer [330 mM Bicine pH 8, 110 mM NaCl, 5.5 mM MgCl2]. Excess Phenol was removed through two subsequent 1 volume chloroform extractions. The final aqueous layer was buffer exchanged into 1.1x SHAPE Folding Buffer or 1.1x DMS Folding Buffer using PD-10 Desalting Columns (GE Healthcare Life Sciences). The resulting RNA solution (3.5 mL nuclear/7 mL cytoplasmic) was incubated at 37 °C for 20 minutes before being split into two equal volumes for control and probe treatment samples.   [5NIA SHAPE probing of extracted RNA]  A 1/10th volume of 10x SHAPE reagent [250 mM 5-nitroisatoic anhydride (5NIA)] in DMSO was added to one sample of RNA while neat DMSO was added to the other. Samples were incubated at 37 °C for 10 minutes.   [DMS probing of extracted RNA]  A 1/10 volume of 10x DMS Solution [1:5 Dimethyl Sulfate (DMS):Ethanol] was added to one sample of RNA while neat ethanol was added to the other. Samples were incubated at 37 °C for 6 minutes. DMS was quenched with 1/5 volume of beta-mercaptoethanol and immediately placed on ice for 5 minutes.  [Precipitation of probe-reacted RNA]  Cell-free RNA was precipitated with 1/10 volume of 2 M NH4OAc and 1 volume of isopropanol. RNA was pelleted at 10,000 x g for 10 minutes at 4 °C. After 1 wash in 75% ethanol, the resulting pellet was dried and then resuspended in 88 µL of water.   [DNase Treatment of cell-derived RNAs]  To 88 µL of in-cell or cell-free RNA samples, 10 µL of 10x TURBO DNase buffer and 4 Units of TURBO DNase (Thermo Fisher) were added and the mixture was incubated at 37 °C for 1 hour. Following this incubation, 2 more Units of TURBO DNase were added and incubation continued at 37 °C for another 1 hour. RNA was purified using a 1.8x ratio of Agencourt RNAClean XP magnetic beads (Beckman Coulter) and eluted into 20-30 µL of nuclease-free water.

value: melanoma short term culture


title: pan_30

value: female


title: 08_0537 A2

type: genomic

city: Durham

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

department: Pathology

institute: Duke University

hyb_protocol: Followed the manufacturer's (Illumina) specifications.

scan_protocol: Followed the manufacturer's (Illumina) specifications on an iScan.

data_processing: Data were interpreted in GenomeStudio v2011.1 Methylation Module 1.9.0 and exported for analysis or were processed in R using ChAMP v. 2.12.4 packages.

label: biotin nucleotide or dinitrophenyl labeled

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications.

extract_protocol: Genomic DNA was extracted using Qiagen All Prep RNA/DNA kit and passed through a Zymo genomic DNA Clean and concentrator kit. Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications.

treatment_protocol: Electroporation of Cas9 for transient expression, flow sorting and single cell dilution.

value: glioma cells

tag: idh1 status


title: C45 DMSO 9Gy 0h

source_name: C45 CTOS, DMSO treated, 0h after 9Gy irradiation


title: 2379-STC1_B

city: Houston

value: H3K9me3 Abcam ab8898


title: SLNCR1 DMS-MaP

description: gene-specific amplicons from total RNA


title: KO-4cell-1

source_name: four cell stage embryos

value: four cell stage embryos


title: pan_29


title: WT-ICM-2


title: IMA_Parental_Replicate2


title: SLNCR1 SHAPE-MaP

description: gene-specific amplicons from total RNA


title: IMA_Parental_Replicate1


title: IMA_Clone4_Replicate2


title: 2357-STC1_G


title: IMA_Clone5_Replicate2

value: -/WT


title: WT-4cell-4


title: KO-4cell-2


title: 2357-STC1_F

value: H3K27me3 Abcam ab6002


title: HEK293T AQ-seq siTUT4/7

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: small RNA-seq

data_processing:
FASTQ files were generated by base-calling using Illumina RTA (v1.18) and conversion using bcl2fastq (v1.8.4).
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the human genome (hg38) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.

growth_protocol: HEK293T and HeLa cells were grown in DMEM media (Welgene) supplemented with 10% FBS (Welgene).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Total RNA was mixed with thirty synthetic miRNA-like spike-in oligos. The RNA mixture was size-fractionated by 15% urea-polyacrylamide gel electrophoresis to enrich miRNA species. Small RNA libraries were constructed using either TruSeq small RNA library preparation kit (Illumina) according to manufacturer's instructions or AQ-seq as follows: miRNA-enriched RNA was ligated to 3′ randomized adapter with 20% PEG 8000, then ligated to 5′ randomized adapter with 20% PEG 8000, reverse-transcribed, and amplified. The cDNA was sequenced using a HiSeq 2500 platform.


title: pan_27


title: HEK293T AQ-seq siNC

description: small RNA-seq


title: C45 DMSO 9Gy 24h

source_name: C45 CTOS, DMSO treated, 24h after 9Gy irradiation


title: KO-4cell-3


title: 2357-STC1_E

value: H3K4me3 Abcam ab8580


title: 08_0537 A4


title: WT-4cell-3


title: 2357-STC1_D

value: H3K79me2 Abcam ab3594


title: pan_05

value: Saline


title: WT-4cell-2


title: 2357-STC1_B


title: pan_04

value: male


title: Cdc45MYC_ChIP_rrm3Dtof1D_AS

city: Geneva

first: Maksym

last: Shyian

state: Geneva

address: 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland

department: Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
For ChIP-Seq raw reads were aligned to the sacCer3  genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
For ChIP-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For ChIP-Seq, the reads were shifted by 100 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: wig and bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

source_name: whole organism

growth_protocol: Asyncrhonous cell culture

extract_protocol:
anti-MYC (Top1-MYC, noMYC, Mcm4-MYC, Cdc45-MYC, Pol2-MYC) ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045)
TruSeq ChIP library preparation kit (Illumina)

treatment_protocol: no treatment

value: W303 MATa RAD5+ bar1D  CDC45-13MYC::HIS3MX6 rrm3D::HPHMX4 tof1D::LEU2

tag: antibody

value: Anti-MYC


title: Pol2MYC_ChIP_rrm3D_AS

value: W303 MATa RAD5+ bar1D FLAG-POL1 POL2-13MYC::KanMX3 rrm3D::HPHMX4


title: 2379-STC1_E

value: Cell Line

tag: chip-antibody


title: Pol2MYC_ChIP_WT_AS

tag: strain

value: W303 MATa RAD5+ bar1D FLAG-POL1 POL2-13MYC::KanMX3


title: pan_07

value: wild type

tag: treatment

value: Pancreas


title: IMA_Clone2_Replicate2


title: IMA_Clone3_Replicate1


title: IMA_Clone1_Replicate2


title: blastocyst_siZcchc8_2

source_name: siZcchc8_blastocyst stage embryos

value: blastocyst stage embryos


title: pan_03

value: female


title: Cdc45MYC_ChIP_rrm3D_AS

value: W303 MATa RAD5+ bar1D  CDC45-13MYC::HIS3MX6 rrm3D::HPHMX4


title: IMA_Clone2_Replicate1

value: glioma cells


title: blastocyst_siZcchc8_1


title: IMA_Parental_DMSO_vehicle_4P


title: Cdc45MYC_ChIP_tof1D_AS

value: W303 MATa RAD5+ bar1D  CDC45-13MYC::HIS3MX6 tof1D::LEU2


title: blastocyst_control_3

source_name: wild type_blastocyst stage embryos


title: IMA_Parental_decitabine_500nM_4P


title: 2173-STC1_E


title: pan_01


title: 2173-STC1_F

value: H3K27me3 Abcam ab6002


title: IMA_Clone5_Replicate1

value: -/WT


title: IMA_Clone1_Replicate1


title: Mcm4MYC_ChIP_rrm3Dtof1D_AS

value: W303 MATa RAD5+ bar1D Mcm4-13MYC::HIS3MX4 rrm3D::HPHMX4 tof1D::LEU2


title: Cdc45MYC_ChIP_WT_AS

value: W303 MATa RAD5+ bar1D  CDC45-13MYC::HIS3MX6


title: Mcm4MYC_ChIP_rrm3D_AS

value: W303 MATa RAD5+ bar1D Mcm4-13MYC::HIS3MX4 rrm3D::HPHMX4


title: 2173-STC1_B

value: H3K9me3 Abcam ab8898


title: blastocyst_control_1


title: input DNA_CS_2212_004

city: Shinjuku

first: Kenta

last: Masui

address: 8-1 Kawada-cho

institute: Tokyo Women's Medical University

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Adapter and low-quality sequences were removed by cutadapt (v1.2.1).
The trimmed reads were aligned to the reference human genome (hg19) using BWA (ver.0.6.2). After that, the reads whose Mapping Quality were zero were removed.
The peaks were called using MACS (ver.1.4.2) with default setting.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated by MACS and wig files were converted to bigwig files using wigToBigWig (v 4). Scores represent the pileup of reads (10 bp resolution).

source_name: Glioblastoma cells

extract_protocol:
Lysates were prepared with SimpleChIPTM Enzymatic Chromatin IP Kit (CST, Beverly, MA) and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the KAPA library preparation kit.

treatment_protocol: U87-EGFRvIII cells were treated with siRNA against Scramble sequence or Rictor (Santa Cruz, Dallas, TX) for 48 hours.

value: glioblastoma cells

tag: RNAi treatment

value: Rictor

tag: chip antibody